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Until recently, the higher-level phylogenetic relationships of coleoid cephalopods have remained unclear. A thorough knowledge of the higher-level phylogeny of the group has been limited by the paucity of paleontological data for this poorly-fossilized group and the lack of cladistic
analyses of developmental, morphological, and molecular data applied to the coleoids. In this study we analyzed a 657 base pair portion of the mitochondrial cytochrome c oxidase I (COI) gene from 48 cephalopod species representing a broad spectrum of coleoid diversity to examine higher-level
phylogenetic relationships within the group. The COI gene exhibited a high degree of nucleotide sequence variability, with one half of the sites varying in at least one taxon. COI amino acid sequences were highly conserved, but were useful in determining basal-level relationships among the
Coleoidea. The evolutionary rate of COI amino acid sequences differed significantly between the two main lineages. The average amino acid sequence divergence within the Octopodiformes was over twice that of the average divergence within the decapods. In addition to analysis of the unweighted
data set, phylogenetic analysis was conducted on the data subjected to a single round of rescaled consistency index (RCI) weighting to reduce the effect of homoplasious substitutions in determining phylogenetic structure. To further reduce the influence of homoplastic change and to facilitate
bootstrap analysis of the data, a nested analysis of the data was employed, beginning with an analysis of the entire data set to determine proper outgroups to be used in the more restrictive analysis of the decapods and octopods separately. We draw the following conclusions from our analysis
of cephalopod COI sequences: (1) the Coleoidea, Octopoda, Vampyromorpha, and Decapoda are monophyletic groups; (2) the Vampyromorpha and Octopoda are sister groups; (3) the Sepioidea, as including the five families Spirulidae, Sepiolidae, Sepiidae, Sepiadariidae, and Idiosepiidae, is polyphyletic;
(4) Spirula is more closely related to the Teuthoidea than it is to the remaining members of the Sepioidea; and (5) the Oegopsida, as currently defined, is polyphyletic.
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